I'd have to see your overall layouts but I think you are on the right track. we build 3 story stacked triplexes and it's very efficient so don't be afraid to go up either. anytime you build more than 1 structure costs are much higher but if its just to offset mortgage and you want to be separate then I understand. 

we just managed to get ong to run all new lines and separate meters for our whole apartment complex at no cost to us. 

I took the Airbnb bookings and now I'm around 80/20 Airbnb/VRBO.Based on a recent bad experience that I had with Airbnb (it's a separate thread out here), I called VRBO and asked them how I can get more booking requests from VRBO. 

You have to separate the two.

It also requires different reporting of that separate interest expense on the K-1 each year so the partners know they have the obligation of tracing that interest expense to however the partner used the distributed proceeds.I typed all this up and realized Mr Brooks has left the building and posted this 6 months ago, but hopefully someone else will find this useful!

They are two separate sales agreements. 

You will receive the security deposit in Checking but then transfer it to Savings.Savings: Hold the deposit here so it's separate from operating funds.

Perhaps we "buy" the house from them for the $328K balance to satisfy the lender and don't need a large down payment and then have a separate contract with them to pay $x per month until we've paid the full $172K amount.

Ideally you would want to transfer the funds you expect to use for the purchase to your new entity for your records to create the separation from personal to business. 

I like that you can setup different virtual accounts for security deposit let's say, or to separately ledger cash collected through a rent to own contract.